Cursoring over the images below will:
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- show two timepoints of a fibroblast deforming a collagen gel
- change magnification where indicated
The Deformation Quantification and Analysis (DQA) software is divided into two parts:
One use of the software is to aid in studying the mechanical effects of cells applying forces within tissue. Users can upload timelapse images showing cell-driven tissue deformations. These deformations should appear in the images as small displacements of the tissue material over time. In our work, we study fibroblasts in or on collagen gels, and the cell-gel configuration is a model tissue.
- Deformation Quantification (tracking) where deformations are automatically detected, quantified and filtered;
- Analysis where tracker output is regularized by singular value decomposition and then analyzed using continuum mechanics to produce output images showing change in 2D density (left above) and strain within the imaged material.
This website provides an on-line interface to the DQA software and contains four areas -- Static, Demo, Real and Beta. At the end of the Static area, a password may be requested to access the other areas. All areas are free of charge. The password is just to control server loading.
At left is a link to each area.
- Static area: allows users to step through the pages of the user interface as they would appear during a demo run, including parameter input and presentation of output. An explanation for each page appears in an adjacent frame. Additionally, users can click on elements within the interface for additional explanations.
- Demo area: provides a pair of demo images. Users can process these images to investigate the software without having to supply their own data.
- Real area: provides full access to the latest validated software and allows users to process their own images.
- Beta area: allows for testing of modifications to DQA and may still be undergoing debugging (currently adding ability to upload a sequence of masks -- not yet working).
Affiliations and Acknowledgements
(1)Steven Vanni was a graduate student in the computational biology program of the Department of Biological Sciences at Carnegie Mellon University. His research interests include living cells as mechanical automata and applications of computer simulation.
(2)Frederick Lanni is an Associate Professor in the Department of Biological Sciences at Carnegie Mellon University. His research interests include mechanisms of cellular force generation and interaction with the extracellular matrix. (e-mail: firstname.lastname@example.org)
We thank David Pane of the Molecular Biosensor and Imaging Center for helping to maintain this website and its server.
We are very fortunate to have had the knowledgeable assistance of the following students:
(3)Matthew Vieta was an undergraduate at Carnegie Mellon University. He engineered the porting of the DQA version 1 from C to C++ as well as implementing the initial web-based user interface now used in the demo and real areas. He also helped with computational testing of the accuracy of the tracker.
(4)Jonathan Lustgarten was an undergraduate at Carnegie Mellon University. He brought frames to the website and implemented the static area. He also helped in investigating optimal values for the tracker parameters.
This work was primarily funded by our Science and Technology Center's NSF grant MCB-8920118.